chr14-69260403-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001168368.2(GALNT16):c.113G>A(p.Arg38Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000574 in 1,603,810 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R38W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001168368.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALNT16 | NM_001168368.2 | c.113G>A | p.Arg38Gln | missense_variant | 1/15 | ENST00000448469.8 | |
GALNT16-AS1 | NR_184249.1 | n.125C>T | non_coding_transcript_exon_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNT16 | ENST00000448469.8 | c.113G>A | p.Arg38Gln | missense_variant | 1/15 | 1 | NM_001168368.2 | P1 | |
ENST00000556316.1 | n.165C>T | non_coding_transcript_exon_variant | 1/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152018Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000434 AC: 1AN: 230416Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 125286
GnomAD4 exome AF: 0.0000613 AC: 89AN: 1451792Hom.: 0 Cov.: 32 AF XY: 0.0000652 AC XY: 47AN XY: 721364
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152018Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74252
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 06, 2023 | The c.113G>A (p.R38Q) alteration is located in exon 1 (coding exon 1) of the GALNT16 gene. This alteration results from a G to A substitution at nucleotide position 113, causing the arginine (R) at amino acid position 38 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at